I have a question rather than a desire... This discussion about the timeline happened in the time of FR/LG & HG/SS? I just assumed that this new stuff makes the old games obsolete and they will be waiting for an update (remake) to feature them again. I mean FR/LF only explanation on why they wasn't any breeding on RBYG was that the daycare couple were living in an island close to johto, but other than that everything appeared from nowhere. Same goes for HG/SS.
Moving this here in order to dissociate the topic from it a bit, and the discussion has gone on long enough in there.
Anyway, that is generally how it would work, and no, there wasn't much discussion about the placement of FRLG or HGSS in the timeline prior to their releases (in fact, until recently we had only the most tenuous of evidence to suggest that FRLG and RSE were contemporaneous, and we don't have that much more even now). However, ORAS is a bit of a different ball game because the actual storyline is being modified in order to accommodate Mega Evolution, which was a moderately big deal in regards to XY's (which take place loooooong after FRLG, which RSE are generally assumed to be contemporaneous with) plot - specifically, the fact that Sycamore says that Mega Evolution is limited to the Kalos region and that not much is known about it. But if ME has been going on in Hoenn this whole time, and if Brendan/May manage to uncover the secrets of ME, then why didn't Sycamore know about it in XY? The simplest solution is to retcon ORAS so that they take place after XY, and that is what is being debated now.